The original action figures were packaged with minicomics, with stories about the characters.[3] In the early comics He-Man is a wandering barbarian on Eternia, a world dealing with the aftermath of a war which devastated its civilizations and left behind fantastic machinery and weapons. The war opened a rift between dimensions, allowing the evil warlord Skeletor to travel to Eternia. Skeletor has set his sights on the ancient Castle Grayskull, a fortress of mystery and power; whoever controls Grayskull will become Master of the Universe. To prevent Skeletor from achieving his goal, He-Man has received special powers and weapons from the Sorceress and defends the castle from Skeletor. He-Man is supported by allies such as Man-At-Arms (the Eternian master of weapons) and Teela, the adopted daughter of Man-At-Arms. Skeletor finds one half of the Power Sword, the key to Castle Grayskull. He-Man received the other half from the Sorceress, and must prevent Skeletor from linking the two halves and gaining access to the castle. To distinguish these stories from the minicomics which were released as tie-ins with the TV series, fans called this first version of Eternia "mini-Eternia" and the words were combined into Mineternia in 2003 by the minicomics fansite Eternia Minor (now He-Man Tales).[4]

With the introduction of Hordak, the minicomics began to diverge from the He-Man and She-Ra animated series and Etheria became Hordak's base of operations.

Years earlier, Hordak had been overthrown by his minion Skeletor and banished from Eternia. He returns, accompanied by the Evil Horde, to conquer the planet. Occasionally allying with Skeletor (but usually attempting to destroy him), Hordak is opposed by He-Man.

In the mini-comic King of the Snakemen, Skeletor discovers a pool of energy buried in Snake Mountain which contains ancient emperor King Hiss. Hiss discloses that he had conquered a number of planets before invading Eternia. Large portions of the planet had fallen to the Snake Men before they were defeated by the Council of the Elders and banished to another dimension. Hiss now seeks to recover his fellow Snake Men and bring vengeance to Eternia.

Details about Eternia's past are revealed in subsequent minicomics surrounding the Three Towers: Grayskull Tower, Viper Tower and Central Tower. The giant structure is raised from underground by Hiss and Skeletor and is the focus of adventures as He-Man tries to prevent all three villains from acquiring the towers' secrets.

Hordak recognises the towers, and claims to have helped build Central Tower. The return of the Towers enhances the Sorceress' magic, and she helps King Randor in his search to discover what happened to his long-lost brother Keldor. Skeletor is determined to stop the search.

Published in the UK by London Edition Magazines, the fortnightly comic series lasted for 72 issues with an additional monthly comic (Masters of the Universe Adventure) running for 28 issues. Storylines included the battle for control of Viper Tower, a team-up of the three villainous factions and the destruction and rebuilding of Eternos. The 'Secret Files of Scrollos' strip featured origin stories for many characters including Sy-Klone, Rio Blast and Snout Spout, and the series included the characters Horde Prime and Scrollos. There was also a short-lived She-Ra comic title, that lasted for 14 issues.

Dark Horse Comics produced minicomics for inclusion in Mattel's Masters of the Universe Classics toy line, continuing the series of minicomics introduced in the 1980s Masters toys. The minicomics were written by Tim Seeley and drawn by Wellinton Alves, with covers by Eric Powell.

According to Seeley, the current minicomics would finish the story planned to be the new direction of the original action-figure line before it was cancelled. The story would deal with the Powers of Grayskull line, which included King Hiss, Tyrantisaurus Rex and He-Ro, tying the toy continuity to the He-Man line and known as The New Adventures of He-Man. Seeley said that the Mattel line intended to blend the He-Man continuities and select the best stories and ideas from MOTU history.[8]

DC took over the Masters of the Universe Classics minicomics in 2012, with artwork by Wellinton Alves and Axel Gimenez. Three issues were published; the first told the origin story of Keldor (Skeletor), the second dealt with He-Man and Skeletor's final battle after their intergalactic New Adventures and the third begins the Son of He-Man era.

In June 2012 DC Comics began publishing a weekly digital title, Masters of the Universe. The first chapter was written by Geoff Johns, with art by Howard Porter and John Livesay. The title planned to explore the world of Eternia, tying into the DC Comics print title He-Man and the Masters of the Universe.[9] DC later announced an ongoing print title.[10]

He-Man and the Masters of the Universe Minicomic Collection (collects all of the Masters of the Universe, Princess of Power, He-Man, and Masters of the Universe Classics minicomics, which originally came with Mattel's toys, 1232 pages, Dark Horse Comics, October 2015)[14]